Microbial-OMICs

This repository holds the metadata schemes for the DZIF microbial OMICs database. The schemes are located in schemes/metaDZIF.yaml. They are implemented in LinkML and are derived from the NFDI4Microbiota metadata standards. So far NGS-based schemes are implemented. Mass-spec related schemes should be released mid of 2024. The scripts in this repository are licensed under MIT license, the schemes are licensed under CC-BY-4.0 license. Please give credit to the work conducted by NFDI4Microbiota and refer to the metadata standards when using the schemes and the DZIF DataHarmonizer.

Insertion of controlled vocabularies into the schemes and building of DZIF DataHarmonizer

To insert ontologies as controlled vocabularies and build the DZIF DataHarmonizer, a fork of the original DataHarmonizer, run the script DataHarmonizerBuilder.py in the src folder after creating a conda environment from the environment.yaml with the flag --repo <name of this repository/folder>. If you are unfamiliar with conda please refer to their documentation for installation.

For setup and activation of the environment:

1. conda env create -f environment.yaml
2. conda activate Microbial-OMICs

After setup and activation of the created conda environment, run this command from the repository folder:

python3 src/DataHarmonizerBuilder.py --repo <name of this repo/folder>

<name of this repo/folder> is the name of the folder this README.md is located in.

The built DZIF DataHarmonizer will be located in the folder DZIFDataHarmonizer and the schemes can be found in the final folder. For a further building process these two folders have to be deleted (or moved) manually.

Updating ontologies

The used ontologies can be updated to a newer version by editing the config/config.yaml file. To start with this, first locate the newest version of the specific ontology using the Ontology Lookup Service (for updating the ROR file for organizations in the collected by field go to the respective zenodo repository) and then insert this information into the config.yaml and push it to the github repository master branch. This should be accompanied by also making a new release of the DZIF DataHarmonizer with an updated version number using semantic versioning. The version of the metadata scheme has to be updated in the metaDZIF.yaml file (changing the version: 1.0.0 to version: 1.1.0, for example) located in the schemes folder.

Funding

This work was funded by the German Center for Infection Research (DZIF).